The goal of this training program is to bring systems engineering students and faculty into the healthcare field through the discipline of clinical informatics, which we believe is a natural fit, and to break down the barriers between systems engineering and healthcare research through close collaboration over common research goals. The National Academy of Engineering (NAE) and Institute of Medicine (IOM) 2005 report entitled "Building a Better Delivery System: A New Engineering/Health Care Partnership" identified system failures in current healthcare delivery and recommended an interdisciplinary approach to solving these problems based on information technology and systems engineering (SE). It identified key barriers to this strategy, including differences between the healthcare and engineering disciplines in "methods, metrics, values and mind-sets." We propose a new strategy for research training in clinical informatics responding directly to the problems identified in the report. This strategy builds on existing successful collaborations between the Department of Systems and Information Engineering in the School of Engineering and Applied Science at the University of Virginia (UVa) and several units in UVa's School of Medicine, including the Division of Clinical Informatics in the Department of Public Health Sciences. Our program creates PhD and postdoctoral training opportunities designed to attract students and established researchers from other fields to address challenging clinical informatics questions. The program inherits a framework from the existing substantial SE graduate program, with unique curricular and research components. The core curriculum includes formal introductions to clinical informatics, SE, and the structure and operation of healthcare delivery systems. Subsequent alternative tracks for training include human-automation interaction, computational statistics and simulation, risk and decision analysis, systems integration, and optimization and control. Research projects are collaborative, with trainees having both healthcare and engineering mentors as they conduct research using systems engineering and medical informatics approaches applicable to improved healthcare delivery and training. We anticipate that this collaborative approach to training will lead to fundamental advances in clinical informatics with a trained set of researchers who will continue to develop the field, thereby addressing the needs articulated by the NAE and IOM.